Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda
Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda
复制标题
线粒体结构重排产生不对称的非适应性突变压力，破坏等足类的系统发育重建
DOI：
10.1093/gbe/evz121
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发表时间：
2019
影响因子：
3.3
通讯作者：
Wang Gui-Tang
中科院分区：
文献类型：
--
作者：
Zhang Dong;Zou Hong;Hua Cong-Jie;Li Wen-Xiang;Mahboob Shahid;Al-Ghanim Khalid Abdullah;Al-Misned Fahad;Jakovlic Ivan;Wang Gui-Tang
等足目是甲壳类动物的一种物种目，其系统发育至今仍未得到解决，不同的数据集（形态、核、线粒体）经常产生明显不一致的系统发育假设。我们假设，它们生活史的极端多样性可能导致线粒体基因组的组成异质性/异缘性，并影响系统发育重建。我们测试了不同数据集（线粒体、核、核苷酸、氨基酸、连接基因、个体基因、基因顺序）、系统发育算法（假设数据同质性、异质性和异缘性）和划分的影响；并发现几乎所有这些都产生了独特的拓扑结构。我们还发现，与其他等足目动物相比，无齿目动物和两个Cymothoidae科（Cymothoidae和Corallanidae）的有丝分裂基因组具有倒碱基（GC）倾斜模式，因此我们得出结论，倒倾斜导致了这些类群之间的长分支吸引系统发育伪像。这些不对称的歪斜很可能是由多个独立的复制起源反转（即，非适应性突变压力）驱动的。尽管PhyloBayes CAT-GTR算法设法减弱了这些伪影（并且优于分割），但线粒体数据在重建等足动物系统发育方面的适用性有限。尽管如此，我们的分析使我们能够为一些尚未解决的系统发育争论提出解决方案，并支持无肢动物是最可能的基础等足类分支的候选者。我们的研究结果表明，即使在相对较短的进化时间尺度上，结构重排也可能产生主要的组成偏差，这意味着通过组成偏差分析证明数据的适用性应该是每一项旨在使用线粒体数据进行系统发育重建的研究的先决条件，即使是在密切相关的分类群中。
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.